We report a method for the preparation of peptide nanofibre gels prepared by a rapid heating/cooling cycle employing electromagnetic radiation heating. An amphiphilic peptide having a C16 chain attached via an esteric link was used as unit for the constructions of the nanofilament network. The thermal history of the peptide amphiphile was traced using differential scanning calorimentry and Hot Stage Microscopy and defines the thermal properties of the monomeric starting material that influence the molecular assemblage in solution. Short microwave burst applied to a dispersion of peptide amphiphiles in water results in the formation of a gel made of branched peptide nanofibres, as the ultrastructure analysis performed by transmission electron microscopy and scanning electron microscopy as shown.